@datagrok/bio 2.11.14 → 2.11.15
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/356.js +2 -0
- package/dist/356.js.map +1 -0
- package/dist/796.js +2 -0
- package/dist/796.js.map +1 -0
- package/dist/8473fcbfb6e85ca6c852.wasm +0 -0
- package/dist/9a8fbf37666e32487835.wasm +0 -0
- package/dist/package-test.js +1 -1
- package/dist/package-test.js.map +1 -1
- package/dist/package.js +1 -1
- package/dist/package.js.map +1 -1
- package/package.json +2 -2
- package/src/package.ts +6 -4
package/package.json
CHANGED
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@@ -5,7 +5,7 @@
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"name": "Leonid Stolbov",
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"email": "lstolbov@datagrok.ai"
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},
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-
"version": "2.11.
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+
"version": "2.11.15",
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"description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
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"repository": {
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"type": "git",
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@@ -36,7 +36,7 @@
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"@biowasm/aioli": "^3.1.0",
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"@datagrok-libraries/bio": "^5.39.10",
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"@datagrok-libraries/chem-meta": "^1.2.1",
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-
"@datagrok-libraries/ml": "^6.3.
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+
"@datagrok-libraries/ml": "^6.3.62",
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"@datagrok-libraries/tutorials": "^1.3.11",
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"@datagrok-libraries/utils": "^4.1.34",
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"cash-dom": "^8.0.0",
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package/src/package.ts
CHANGED
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@@ -246,6 +246,7 @@ export function SequenceSpaceEditor(call: DG.FuncCall) {
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plotEmbeddings: params.plotEmbeddings,
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options: params.options,
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preprocessingFunction: params.preprocessingFunction,
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clusterEmbeddings: params.clusterEmbeddings,
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}).call();
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})
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.show();
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@@ -493,7 +494,7 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column<
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//tags: dim-red-preprocessing-function
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//meta.supportedSemTypes: Macromolecule
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//meta.supportedTypes: string
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-
//meta.supportedUnits: fasta,separator
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//meta.supportedUnits: fasta,separator,helm
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//meta.supportedDistanceFunctions: Hamming,Levenshtein,Monomer chemical distance,Needlemann-Wunsch
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//input: column col {semType: Macromolecule}
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//input: string metric
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@@ -541,19 +542,20 @@ export async function helmPreprocessingFunction(
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//input: bool plotEmbeddings = true
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//input: func preprocessingFunction {optional: true}
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//input: object options {optional: true}
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+
//input: bool clusterEmbeddings = true { optional: true }
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//output: viewer result
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//editor: Bio:SequenceSpaceEditor
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export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Column,
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methodName: DimReductionMethods, similarityMetric: BitArrayMetrics | MmDistanceFunctionsNames,
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-
plotEmbeddings: boolean, preprocessingFunction?: DG.Func, options?: (IUMAPOptions | ITSNEOptions) & Options
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-
): Promise<DG.ScatterPlotViewer | undefined> {
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plotEmbeddings: boolean, preprocessingFunction?: DG.Func, options?: (IUMAPOptions | ITSNEOptions) & Options,
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clusterEmbeddings?: boolean): Promise<DG.ScatterPlotViewer | undefined> {
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if (!checkInputColumnUI(molecules, 'Sequence Space'))
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return;
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if (!preprocessingFunction)
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preprocessingFunction = DG.Func.find({name: 'macromoleculePreprocessingFunction', package: 'Bio'})[0];
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const res = await reduceDimensionality(table, molecules, methodName,
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similarityMetric as KnownMetrics, preprocessingFunction, plotEmbeddings, options, {
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similarityMetric as KnownMetrics, preprocessingFunction, plotEmbeddings, clusterEmbeddings ?? false, options, {
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fastRowCount: 10000,
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scatterPlotName: 'Sequence space',
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bypassLargeDataWarning: options?.[BYPASS_LARGE_DATA_WARNING],
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